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[Bioc-devel] Problem Mogene10stprobeset

2 messages · jarod_v6 at libero.it, James W. MacDonald

Original
jarod_v6 at libero.it
# 
Hi there!!!
 I'm a student and I want to learn how to use bioconductor but I have this 
problem  
I use this script for  analysis the data  starting from .CEL data. After I 
prepare  annotated gene I found annotate only 91 gene... I don't Understand why 
happed that.
Someone Can Help Me?

source("http://www.bioconductor.org/biocLite.R")
biocLite("affy")
biocLite("limma")
biocLite("annotate")
biocLite("mogene10stprobeset.db")
install.packages("R2HTML")


library(affy)
library(limma)
library(annotate)
library("mogene10stprobeset.db")
library(R2HTML)

data<-ReadAffy()
eset <- rma(data)
class(eset)
eset at annotation

# Get the transcript cluster IDs from the expressionset
ID <- featureNames(eset)
Symbol <- getSYMBOL(ID, "mogene10stprobeset.db")
Name <- as.character(lookUp(ID, "mogene10stprobeset.db", "GENENAME"))
Ensembl <- as.character(lookUp(ID, "mogene10stprobeset.db", "ENSEMBL"))
luisa<-exprs(eset) 
martina<-data.frame(ID=ID,Symbol=Symbol, Name=Name, Ensembl=Ensembl,
geee=luisa, stringsAsFactors=F)
martina[martina=="NA"] <- NA
write.table(martina,"DAti_an.csv",sep="\t")


It is annotatet only the last 91 ID....Why?

Thanks in advance for any Help
M.
James W. MacDonald
#
On 6/21/2012 9:33 AM, jarod_v6 at libero.it wrote:
Since you are using the affy package to process these data, you are 
summarizing at the transcript level rather than the probeset level. So 
you want the mogene10sttranscriptcluster.db package.

Best,

Jim